Pre-visualization of the normalized count data before any differential analysis
Table of content
Warning message in is.na(x[[i]]): “is.na() applied to non-(list or vector) of type 'environment'”Warning message in rsqlite_fetch(res@ptr, n = n): “Don't need to call dbFetch() for statements, only for queries”
========================================================================== * * Package WGCNA 1.63 loaded. * * Important note: It appears that your system supports multi-threading, * but it is not enabled within WGCNA in R. * To allow multi-threading within WGCNA with all available cores, use * * allowWGCNAThreads() * * within R. Use disableWGCNAThreads() to disable threading if necessary. * Alternatively, set the following environment variable on your system: * * ALLOW_WGCNA_THREADS=<number_of_processors> * * for example * * ALLOW_WGCNA_THREADS=4 * * To set the environment variable in linux bash shell, type * * export ALLOW_WGCNA_THREADS=4 * * before running R. Other operating systems or shells will * have a similar command to achieve the same aim. * ========================================================================== Allowing multi-threading with up to 4 threads. [1] "preparing gene to GO mapping data..." [1] "preparing IC data..." [1] "preparing gene to GO mapping data..." [1] "preparing IC data..." [1] "preparing gene to GO mapping data..." [1] "preparing IC data..."
pickSoftThreshold: will use block size 4347. pickSoftThreshold: calculating connectivity for given powers... ..working on genes 1 through 4347 of 10291 ..working on genes 4348 through 8694 of 10291 ..working on genes 8695 through 10291 of 10291 Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k. 1 1 0.227 1.310 0.952 1030.000 1.03e+03 1570.0 2 2 0.232 -0.842 0.911 328.000 3.12e+02 758.0 3 3 0.590 -1.550 0.954 132.000 1.15e+02 446.0 4 4 0.729 -1.880 0.974 61.300 4.74e+01 292.0 5 5 0.771 -2.080 0.972 31.700 2.12e+01 205.0 6 6 0.812 -2.130 0.981 17.800 1.01e+01 150.0 7 7 0.802 -2.220 0.974 10.600 5.05e+00 114.0 8 8 0.831 -2.190 0.983 6.630 2.61e+00 88.7 9 9 0.852 -2.140 0.988 4.330 1.40e+00 70.5 10 10 0.867 -2.110 0.991 2.920 7.74e-01 56.8 11 12 0.872 -2.060 0.983 1.440 2.55e-01 38.4 12 14 0.877 -2.010 0.977 0.779 9.07e-02 26.9 13 16 0.893 -1.940 0.982 0.449 3.40e-02 19.4 14 18 0.906 -1.860 0.985 0.273 1.33e-02 14.2 15 20 0.929 -1.780 0.993 0.173 5.31e-03 10.7
| Power | SFT.R.sq | slope | truncated.R.sq | mean.k. | median.k. | max.k. |
|---|---|---|---|---|---|---|
| 1 | 0.2273633 | 1.3069408 | 0.9522773 | 1032.2103062 | 1.031743e+03 | 1574.40467 |
| 2 | 0.2318240 | -0.8419065 | 0.9109768 | 328.3750082 | 3.124206e+02 | 758.22758 |
| 3 | 0.5898524 | -1.5468341 | 0.9541521 | 131.7106717 | 1.147058e+02 | 446.45478 |
| 4 | 0.7293365 | -1.8760203 | 0.9740987 | 61.3157190 | 4.736691e+01 | 292.33277 |
| 5 | 0.7706350 | -2.0775848 | 0.9724795 | 31.7270126 | 2.117472e+01 | 204.76919 |
| 6 | 0.8116126 | -2.1271367 | 0.9807292 | 17.7731786 | 1.008260e+01 | 150.23963 |
| 7 | 0.8022879 | -2.2224796 | 0.9735875 | 10.5925115 | 5.050971e+00 | 114.00564 |
| 8 | 0.8307511 | -2.1879600 | 0.9827800 | 6.6345171 | 2.608895e+00 | 88.74112 |
| 9 | 0.8519550 | -2.1423593 | 0.9884310 | 4.3282040 | 1.397797e+00 | 70.46121 |
| 10 | 0.8665930 | -2.1052573 | 0.9914710 | 2.9212252 | 7.738615e-01 | 56.84323 |
| 12 | 0.8724663 | -2.0611029 | 0.9830544 | 1.4447620 | 2.552006e-01 | 38.38129 |
| 14 | 0.8766131 | -2.0101797 | 0.9767692 | 0.7788890 | 9.066889e-02 | 26.89092 |
| 16 | 0.8933757 | -1.9356365 | 0.9817629 | 0.4488075 | 3.402853e-02 | 19.36386 |
| 18 | 0.9058564 | -1.8638594 | 0.9845667 | 0.2726832 | 1.328237e-02 | 14.24265 |
| 20 | 0.9285263 | -1.7822036 | 0.9931630 | 0.1729982 | 5.314736e-03 | 10.65525 |
| Power | mean.k. | |
|---|---|---|
| 6 | 6 | 17.7731786 |
| 7 | 7 | 10.5925115 |
| 8 | 8 | 6.6345171 |
| 9 | 9 | 4.3282040 |
| 10 | 10 | 2.9212252 |
| 11 | 12 | 1.4447620 |
| 12 | 14 | 0.7788890 |
| 13 | 16 | 0.4488075 |
| 14 | 18 | 0.2726832 |
| 15 | 20 | 0.1729982 |
Parameters for network construction
Calculating module eigengenes block-wise from all genes
Flagging genes and samples with too many missing values...
..step 1
..Working on block 1 .
TOM calculation: adjacency..
..will use 4 parallel threads.
Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..saving TOM for block 1 into file norm_genes_TOM-block.1.RData
....clustering..
....detecting modules..
....calculating module eigengenes..
....checking kME in modules..
..removing 1 genes from module 1 because their KME is too low.
..removing 3 genes from module 9 because their KME is too low.
..removing 1 genes from module 12 because their KME is too low.
..removing 1 genes from module 13 because their KME is too low.
..merging modules that are too close..
mergeCloseModules: Merging modules whose distance is less than 0.35
Calculating new MEs...
ME0 ME1 ME2 ME3 ME4 ME5 ME6 ME7 ME8 ME9 ME10 ME11 4663 1239 1082 630 595 552 476 367 315 178 139 55
Percentages of XY genes per modules
[1] "0: 147 - 3.15247694617199%" [1] "1: 36 - 2.90556900726392%" [1] "2: 53 - 4.89833641404806%" [1] "3: 18 - 2.85714285714286%" [1] "4: 13 - 2.18487394957983%" [1] "5: 19 - 3.44202898550725%" [1] "6: 9 - 1.89075630252101%" [1] "7: 7 - 1.90735694822888%" [1] "8: 9 - 2.85714285714286%" [1] "9: 2 - 1.12359550561798%" [1] "10: 1 - 0.719424460431655%" [1] "11: 1 - 1.81818181818182%"
The mean of the Z-score over the samples in the group is plot for each gene
[1] "0"
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 1495 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
9622 GO:0034641 1.930318e-34 1 1689
11864 GO:0044237 1.819262e-33 1 2515
9636 GO:0034660 1.511191e-32 1 212
11881 GO:0044260 2.808359e-32 1 2109
2983 GO:0006139 6.603118e-32 1 1518
9532 GO:0034470 7.640556e-32 1 169
numInCat term ontology
9622 5285 cellular nitrogen compound metabolic process BP
11864 8386 cellular metabolic process BP
9636 405 ncRNA metabolic process BP
11881 6844 cellular macromolecule metabolic process BP
2983 4672 nucleobase-containing compound metabolic process BP
9532 301 ncRNA processing BP
[1] "1"
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 1495 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
17661 GO:0090304 3.630391e-20 1 450
11881 GO:0044260 1.095788e-18 1 644
5710 GO:0016070 1.118447e-17 1 406
2983 GO:0006139 9.921890e-17 1 468
12852 GO:0046483 4.487238e-16 1 471
11364 GO:0043170 1.928903e-15 1 667
numInCat term ontology
17661 4172 nucleic acid metabolic process BP
11881 6844 cellular macromolecule metabolic process BP
5710 3729 RNA metabolic process BP
2983 4672 nucleobase-containing compound metabolic process BP
12852 4765 heterocycle metabolic process BP
11364 7455 macromolecule metabolic process BP
[1] "2"
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 1495 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
12259 GO:0045184 9.868354e-13 1 181
11879 GO:0044257 1.106652e-12 1 84
14123 GO:0051234 2.182943e-12 1 345
5312 GO:0015031 2.460062e-12 1 167
13314 GO:0048193 2.934615e-12 1 40
3431 GO:0006810 4.433883e-12 1 333
numInCat term ontology
12259 1765 establishment of protein localization BP
11879 604 cellular protein catabolic process BP
14123 4062 establishment of localization BP
5312 1606 protein transport BP
13314 185 Golgi vesicle transport BP
3431 3915 transport BP
[1] "3"
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 1495 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
17661 GO:0090304 8.971982e-19 1 245
5710 GO:0016070 1.893249e-17 1 223
14136 GO:0051252 2.138832e-15 1 190
2983 GO:0006139 5.935538e-15 1 251
12852 GO:0046483 7.973750e-15 1 254
14083 GO:0051171 1.403879e-14 1 210
numInCat term ontology
17661 4172 nucleic acid metabolic process BP
5710 3729 RNA metabolic process BP
14136 3046 regulation of RNA metabolic process BP
2983 4672 nucleobase-containing compound metabolic process BP
12852 4765 heterocycle metabolic process BP
14083 3601 regulation of nitrogen compound metabolic process BP
[1] "4"
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations... For 1495 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
11864 GO:0044237 3.108584e-18 1 368
16807 GO:0071704 1.641624e-16 1 377
11881 GO:0044260 1.908849e-16 1 307
3934 GO:0008152 1.988270e-16 1 390
11865 GO:0044238 2.158860e-16 1 361
11364 GO:0043170 2.641483e-16 1 328
numInCat term ontology
11864 8386 cellular metabolic process BP
16807 8831 organic substance metabolic process BP
11881 6844 cellular macromolecule metabolic process BP
3934 9217 metabolic process BP
11865 8362 primary metabolic process BP
11364 7455 macromolecule metabolic process BP
[1] "5"
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations... For 1495 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
3553 GO:0007005 4.130830e-20 1 70
3934 GO:0008152 1.159491e-17 1 342
14836 GO:0055114 5.773753e-16 1 76
11864 GO:0044237 7.659119e-16 1 309
3431 GO:0006810 8.277589e-16 1 167
14123 GO:0051234 1.090689e-14 1 167
numInCat term ontology
3553 611 mitochondrion organization BP
3934 9217 metabolic process BP
14836 836 oxidation-reduction process BP
11864 8386 cellular metabolic process BP
3431 3915 transport BP
14123 4062 establishment of localization BP
[1] "6"
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations... For 1495 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
12058 GO:0044710 6.653859e-23 1 174
4336 GO:0009056 3.116046e-13 1 88
12060 GO:0044712 4.296236e-13 1 52
18752 GO:1901575 4.041497e-12 1 83
3934 GO:0008152 1.327891e-11 1 306
2882 GO:0005975 1.537646e-11 1 41
numInCat term ontology
12058 3280 single-organism metabolic process BP
4336 1533 catabolic process BP
12060 635 single-organism catabolic process BP
18752 1478 organic substance catabolic process BP
3934 9217 metabolic process BP
2882 489 carbohydrate metabolic process BP
[1] "7"
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 1495 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
13833 GO:0050794 2.673494e-09 1 248
6626 GO:0019222 1.600242e-08 1 167
5710 GO:0016070 2.997303e-08 1 129
7965 GO:0031323 3.075312e-08 1 159
13829 GO:0050789 4.088212e-08 1 253
11881 GO:0044260 4.439255e-08 1 201
numInCat term ontology
13833 8793 regulation of cellular process BP
6626 5208 regulation of metabolic process BP
5710 3729 RNA metabolic process BP
7965 4897 regulation of cellular metabolic process BP
13829 9278 regulation of biological process BP
11881 6844 cellular macromolecule metabolic process BP
[1] "8"
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations... For 1495 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
3523 GO:0006955 2.985898e-25 1 70
1046 GO:0002376 3.655761e-25 1 100
3520 GO:0006952 1.989081e-22 1 72
12206 GO:0045087 7.941872e-22 1 47
11393 GO:0043207 2.651971e-17 1 49
14391 GO:0051707 2.651971e-17 1 49
numInCat term ontology
3523 982 immune response BP
1046 1975 immune system process BP
3520 1156 defense response BP
12206 500 innate immune response BP
11393 686 response to external biotic stimulus BP
14391 686 response to other organism BP
[1] "9"
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 1495 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
1211 GO:0002682 2.613030e-07 0.9999999 30
1213 GO:0002684 2.877916e-07 0.9999999 23
952 GO:0002221 1.182405e-06 0.9999999 9
7990 GO:0031349 1.266030e-06 0.9999998 13
1267 GO:0002758 1.395896e-06 0.9999999 9
13445 GO:0048518 1.634916e-06 0.9999992 77
numInCat term ontology
1211 1088 regulation of immune system process BP
1213 676 positive regulation of immune system process BP
952 104 pattern recognition receptor signaling pathway BP
7990 252 positive regulation of defense response BP
1267 106 innate immune response-activating signal transduction BP
13445 4751 positive regulation of biological process BP
[1] "10"
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 1495 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
[1] category over_represented_pvalue under_represented_pvalue [4] numDEInCat numInCat term [7] ontology <0 rows> (or 0-length row.names) [1] "11"
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 1495 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
[1] category over_represented_pvalue under_represented_pvalue [4] numDEInCat numInCat term [7] ontology <0 rows> (or 0-length row.names)
TOM calculation: adjacency.. ..will use 4 parallel threads. Fraction of slow calculations: 0.000000 ..connectivity.. ..matrix multiplication (system BLAS).. ..normalization.. ..done.
| 0610007P14Rik | 0610009B22Rik | 0610009O20Rik | 0610010K14Rik | 0610030E20Rik | 0610037L13Rik | Fmc1 | Card19 | 1110008F13Rik | 1110008P14Rik | ⋯ | Zswim7 | Zswim8 | Zufsp | Zwint | Zxda | Zyg11b | Zyx | Zzef1 | Zzz3 | Hikeshi | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0610007P14Rik | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | ⋯ | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 0610009B22Rik | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ⋯ | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| 0610009O20Rik | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | ⋯ | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| 0610010K14Rik | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | ⋯ | 1 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 1 |
| 0610030E20Rik | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 1 | 0 | ⋯ | 0 | 1 | 1 | 1 | 0 | 1 | 0 | 1 | 1 | 0 |
| 0610037L13Rik | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | ⋯ | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 1 | 1 | 0 |